diff --git a/core/src/main/scala/org/apache/spark/util/Vector.scala b/core/src/main/scala/org/apache/spark/util/Vector.scala
deleted file mode 100644
index 6b3fa8491904a..0000000000000
--- a/core/src/main/scala/org/apache/spark/util/Vector.scala
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License.  You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.apache.spark.util
-
-import scala.language.implicitConversions
-import scala.util.Random
-
-import org.apache.spark.util.random.XORShiftRandom
-
-@deprecated("Use Vectors.dense from Spark's mllib.linalg package instead.", "1.0.0")
-class Vector(val elements: Array[Double]) extends Serializable {
-  def length: Int = elements.length
-
-  def apply(index: Int): Double = elements(index)
-
-  def + (other: Vector): Vector = {
-    if (length != other.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    Vector(length, i => this(i) + other(i))
-  }
-
-  def add(other: Vector): Vector = this + other
-
-  def - (other: Vector): Vector = {
-    if (length != other.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    Vector(length, i => this(i) - other(i))
-  }
-
-  def subtract(other: Vector): Vector = this - other
-
-  def dot(other: Vector): Double = {
-    if (length != other.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    var ans = 0.0
-    var i = 0
-    while (i < length) {
-      ans += this(i) * other(i)
-      i += 1
-    }
-    ans
-  }
-
-  /**
-   * return (this + plus) dot other, but without creating any intermediate storage
-   * @param plus
-   * @param other
-   * @return
-   */
-  def plusDot(plus: Vector, other: Vector): Double = {
-    if (length != other.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    if (length != plus.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    var ans = 0.0
-    var i = 0
-    while (i < length) {
-      ans += (this(i) + plus(i)) * other(i)
-      i += 1
-    }
-    ans
-  }
-
-  def += (other: Vector): Vector = {
-    if (length != other.length) {
-      throw new IllegalArgumentException("Vectors of different length")
-    }
-    var i = 0
-    while (i < length) {
-      elements(i) += other(i)
-      i += 1
-    }
-    this
-  }
-
-  def addInPlace(other: Vector): Vector = this +=other
-
-  def * (scale: Double): Vector = Vector(length, i => this(i) * scale)
-
-  def multiply (d: Double): Vector = this * d
-
-  def / (d: Double): Vector = this * (1 / d)
-
-  def divide (d: Double): Vector = this / d
-
-  def unary_- : Vector = this * -1
-
-  def sum: Double = elements.reduceLeft(_ + _)
-
-  def squaredDist(other: Vector): Double = {
-    var ans = 0.0
-    var i = 0
-    while (i < length) {
-      ans += (this(i) - other(i)) * (this(i) - other(i))
-      i += 1
-    }
-    ans
-  }
-
-  def dist(other: Vector): Double = math.sqrt(squaredDist(other))
-
-  override def toString: String = elements.mkString("(", ", ", ")")
-}
-
-@deprecated("Use Vectors.dense from Spark's mllib.linalg package instead.", "1.0.0")
-object Vector {
-  def apply(elements: Array[Double]): Vector = new Vector(elements)
-
-  def apply(elements: Double*): Vector = new Vector(elements.toArray)
-
-  def apply(length: Int, initializer: Int => Double): Vector = {
-    val elements: Array[Double] = Array.tabulate(length)(initializer)
-    new Vector(elements)
-  }
-
-  def zeros(length: Int): Vector = new Vector(new Array[Double](length))
-
-  def ones(length: Int): Vector = Vector(length, _ => 1)
-
-  /**
-   * Creates this [[org.apache.spark.util.Vector]] of given length containing random numbers
-   * between 0.0 and 1.0. Optional scala.util.Random number generator can be provided.
-   */
-  def random(length: Int, random: Random = new XORShiftRandom()): Vector =
-    Vector(length, _ => random.nextDouble())
-
-  class Multiplier(num: Double) {
-    def * (vec: Vector): Vector = vec * num
-  }
-
-  implicit def doubleToMultiplier(num: Double): Multiplier = new Multiplier(num)
-
-  implicit object VectorAccumParam extends org.apache.spark.AccumulatorParam[Vector] {
-    def addInPlace(t1: Vector, t2: Vector): Vector = t1 + t2
-
-    def zero(initialValue: Vector): Vector = Vector.zeros(initialValue.length)
-  }
-
-}
diff --git a/core/src/test/scala/org/apache/spark/util/VectorSuite.scala b/core/src/test/scala/org/apache/spark/util/VectorSuite.scala
deleted file mode 100644
index 11194cd22a419..0000000000000
--- a/core/src/test/scala/org/apache/spark/util/VectorSuite.scala
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License.  You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.apache.spark.util
-
-import scala.util.Random
-
-import org.apache.spark.SparkFunSuite
-
-/**
- * Tests org.apache.spark.util.Vector functionality
- */
-@deprecated("suppress compile time deprecation warning", "1.0.0")
-class VectorSuite extends SparkFunSuite {
-
-  def verifyVector(vector: Vector, expectedLength: Int): Unit = {
-    assert(vector.length == expectedLength)
-    assert(vector.elements.min > 0.0)
-    assert(vector.elements.max < 1.0)
-  }
-
-  test("random with default random number generator") {
-    val vector100 = Vector.random(100)
-    verifyVector(vector100, 100)
-  }
-
-  test("random with given random number generator") {
-    val vector100 = Vector.random(100, new Random(100))
-    verifyVector(vector100, 100)
-  }
-}
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala b/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala
deleted file mode 100644
index eaa71dad17a04..0000000000000
--- a/graphx/src/main/scala/org/apache/spark/graphx/GraphKryoRegistrator.scala
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License.  You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.apache.spark.graphx
-
-import com.esotericsoftware.kryo.Kryo
-
-import org.apache.spark.graphx.impl._
-import org.apache.spark.graphx.util.collection.GraphXPrimitiveKeyOpenHashMap
-import org.apache.spark.serializer.KryoRegistrator
-import org.apache.spark.util.BoundedPriorityQueue
-import org.apache.spark.util.collection.BitSet
-import org.apache.spark.util.collection.OpenHashSet
-
-/**
- * Registers GraphX classes with Kryo for improved performance.
- */
-@deprecated("Register GraphX classes with Kryo using GraphXUtils.registerKryoClasses", "1.2.0")
-class GraphKryoRegistrator extends KryoRegistrator {
-
-  def registerClasses(kryo: Kryo) {
-    kryo.register(classOf[Edge[Object]])
-    kryo.register(classOf[(VertexId, Object)])
-    kryo.register(classOf[EdgePartition[Object, Object]])
-    kryo.register(classOf[BitSet])
-    kryo.register(classOf[VertexIdToIndexMap])
-    kryo.register(classOf[VertexAttributeBlock[Object]])
-    kryo.register(classOf[PartitionStrategy])
-    kryo.register(classOf[BoundedPriorityQueue[Object]])
-    kryo.register(classOf[EdgeDirection])
-    kryo.register(classOf[GraphXPrimitiveKeyOpenHashMap[VertexId, Int]])
-    kryo.register(classOf[OpenHashSet[Int]])
-    kryo.register(classOf[OpenHashSet[Long]])
-  }
-}
diff --git a/project/MimaExcludes.scala b/project/MimaExcludes.scala
index 940fedfa2ab60..43ca4690dc2bb 100644
--- a/project/MimaExcludes.scala
+++ b/project/MimaExcludes.scala
@@ -112,6 +112,13 @@ object MimaExcludes {
         ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.api.java.JavaSparkContext.defaultMinSplits"),
         ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.api.java.JavaSparkContext.clearJars"),
         ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.api.java.JavaSparkContext.clearFiles")
+      ) ++
+      // SPARK-12665 Remove deprecated and unused classes
+      Seq(
+        ProblemFilters.exclude[MissingClassProblem]("org.apache.spark.graphx.GraphKryoRegistrator"),
+        ProblemFilters.exclude[MissingClassProblem]("org.apache.spark.util.Vector"),
+        ProblemFilters.exclude[MissingClassProblem]("org.apache.spark.util.Vector$Multiplier"),
+        ProblemFilters.exclude[MissingClassProblem]("org.apache.spark.util.Vector$")
       )
     case v if v.startsWith("1.6") =>
       Seq(