diff --git a/MOcov/@MOcovMFileCollection/MOcovMFileCollection.m b/MOcov/@MOcovMFileCollection/MOcovMFileCollection.m
index dec91ed..93a2708 100644
--- a/MOcov/@MOcovMFileCollection/MOcovMFileCollection.m
+++ b/MOcov/@MOcovMFileCollection/MOcovMFileCollection.m
@@ -1,4 +1,4 @@
-function obj=MOcovMFileCollection(root_dir, method, monitor)
+function obj=MOcovMFileCollection(root_dir, method, monitor, exclude_pat)
 % instantiate MOcovMFileCollection
 %
 % obj=MOcovMFileCollection(root_dir, method, monitor)
@@ -13,9 +13,14 @@
 %                           - 'profile' use Matlab profiler
 %                           default: 'file'
 %   monitor                 optional MOcovProgressMonitor instance
+%   exclude_pat             Optional cell array of patterns to exclude.
 %
 % See also: mocov
 
+    if nargin<4 || isempty(exclude_pat)
+        exclude_pat={};
+    end
+
     if nargin<3 || isempty(monitor)
         monitor=MOcovProgressMonitor();
     end
@@ -27,6 +32,7 @@
     props=struct();
     props.root_dir=root_dir;
     props.monitor=monitor;
+    props.exclude_pat=exclude_pat;
     props.mfiles=[];
     props.orig_path=[];
     props.temp_dir=[];
diff --git a/MOcov/@MOcovMFileCollection/prepare.m b/MOcov/@MOcovMFileCollection/prepare.m
index b3a470e..615c634 100644
--- a/MOcov/@MOcovMFileCollection/prepare.m
+++ b/MOcov/@MOcovMFileCollection/prepare.m
@@ -14,7 +14,7 @@
 
     monitor=obj.monitor;
 
-    fns=mocov_find_files(obj.root_dir,'*.m',monitor);
+    fns=mocov_find_files(obj.root_dir,'*.m',monitor,obj.exclude_pat);
     n=numel(fns);
 
     mfiles=cell(n,1);
diff --git a/MOcov/mocov.m b/MOcov/mocov.m
index c8baf14..6155df4 100644
--- a/MOcov/mocov.m
+++ b/MOcov/mocov.m
@@ -16,6 +16,10 @@
 %                               Mutually exclusive with '-e' option.
 %   '-cover', covd              Find coverage for files in dir covd and all
 %                               of its subdirectories
+%   '-cover_exclude', pat       (optional) Exclude files and directories
+%                               which match this pattern, even if they are
+%                               in covd. Can be used multiple times to
+%                               specify multiple patterns to match.
 %   '-cover_json_file', cj      (optional) Store coverage information in
 % `                             file cj in JSON format [use with coveralls]
 %   '-cover_xml_file', xc       (optional) Store coverage information in
@@ -81,7 +85,8 @@
     monitor=MOcovProgressMonitor(opt.verbose);
     mfile_collection=MOcovMFileCollection(opt.cover,...
                                                     opt.method,...
-                                                    monitor);
+                                                    monitor,...
+                                                    opt.excludes);
     mfile_collection=prepare(mfile_collection);
     cleaner_collection=onCleanup(@()cleanup(mfile_collection));                                                    
 
@@ -151,6 +156,7 @@ function write_coverage_results(writers, mfile_collection, opt)
 
     defaults=struct();
     defaults.coverage_dir=pwd();
+    defaults.excludes={};
     defaults.html_dir=[];
     defaults.cobertura_xml=[];
     defaults.coveralls_json=[];
@@ -185,6 +191,10 @@ function write_coverage_results(writers, mfile_collection, opt)
                     k=k+1;
                     opt.cover=varargin{k};
 
+                case '-cover_exclude'
+                    k=k+1;
+                    opt.excludes(end+1)=varargin(k);
+
                 case '-verbose'
                     opt.verbose=opt.verbose+1;
 
diff --git a/MOcov/mocov_find_files.m b/MOcov/mocov_find_files.m
index e8b9d03..f6c2e24 100644
--- a/MOcov/mocov_find_files.m
+++ b/MOcov/mocov_find_files.m
@@ -1,4 +1,4 @@
-function res=mocov_find_files(root_dir, file_pat, monitor)
+function res=mocov_find_files(root_dir, file_pat, monitor, exclude_pat)
 % Finds files recursively in a directory
 %
 % res=mocov_find_files([root_dir[, file_pat]])
@@ -12,6 +12,9 @@
 %                       is used, corresponding to all files.
 %   monitor             Optional progress monitory that supports a
 %                       'notify' method.
+%   exclude_pat         Optional cell array of patterns to exclude. Both
+%                       files and directories which match one of these
+%                       patterns will be omitted from the output.
 %
 % Output:
 %   res                 Kx1 cell with names of files in root_dir matching
@@ -35,10 +38,28 @@
         monitor=[];
     end
 
+    if nargin<4
+        exclude_pat={};
+    end
+
+    if ischar(exclude_pat)
+        exclude_pat={exclude_pat};
+    end
+
     file_re=['^' ... % start of the string
              regexptranslate('wildcard',file_pat) ...
              '$'];   % end of the string
 
+     exclude_re='';
+     for k=1:numel(exclude_pat)
+         if ~isempty(exclude_re)
+             exclude_re=[exclude_re '|'];
+         end
+         exclude_re=[exclude_re ...
+                     '^' ... % start of the string
+                     regexptranslate('wildcard',exclude_pat{k}) ...
+                     '$'];   % end of the string
+     end
 
     if ~isempty(monitor)
         msg=sprintf('Finding files matching %s from %s',file_pat,root_dir);
@@ -47,7 +68,7 @@
 
     res=find_files_recursively(root_dir,file_re,monitor);
 
-function res=find_files_recursively(root_dir,file_re,monitor)
+function res=find_files_recursively(root_dir,file_re,monitor,exclude_re)
     if isempty(root_dir)
         dir_arg={};
     else
@@ -67,8 +88,10 @@
         if ~ignore_fn
             path_fn=fullfile(root_dir, fn);
 
-            if isdir(path_fn)
-                res=find_files_recursively(path_fn,file_re,monitor);
+            if ~isempty(regexp(fn,exclude_re,'once'));
+                continue;
+            elseif isdir(path_fn)
+                res=find_files_recursively(path_fn,file_re,monitor,exclude_re);
             elseif ~isempty(regexp(fn,file_re,'once'));
                 res={path_fn};
                 if ~isempty(monitor)
@@ -79,4 +102,4 @@
         res_cell{k}=res;
     end
 
-    res=cat(1,res_cell{:});
\ No newline at end of file
+    res=cat(1,res_cell{:});