Stephen's natsort is useful: FileList = dir(fullfile(Folder, '*.*')); [~, Index] = natsort({FileList.name}); FileList = FileList(Index); If the file extensions should not influence the sorting order, use |natsortfiles| from the same link.

natsortfiles is not an inbuilt MATLAB function: you must download it, unzip it, and put both Mfiles on your MATLAB Search Path (e.g. in the current directory). Then simply use it to sort the output from DIR: S = dir(..): S = natsortfiles(S); % alphanumeric sort by filename ... your code Note that the correct function name is natsortfiles, not natsortfile (as you have in your title).

You could download my FEX submission natsortfiles: http://www.mathworks.com/matlabcentral/fileexchange/47434-natural-order-filename-sort and use it to directly sort the output from DIR: allFiles = natsortfiles(dir('*.txt')); The function natsortfiles does not perform a naive natural-order sort, but also sorts the filenames and file extensions separately so that the file extension period character does not influence the sort output: >> A = {'doc_10.txt'; 'doc_20.txt'; 'doc_2.txt'; 'doc_1.txt'; 'doc_11.txt'}; >> sort(A) % gives the wrong order! ans = 'doc_1.txt' 'doc_10.txt' 'doc_11.txt' 'doc_2.txt' 'doc_20.txt' >> natsortfiles(A) % the correct number order :) ans = 'doc_1.txt' 'doc_2.txt' 'doc_10.txt' 'doc_11.txt' 'doc_20.txt'

You could download my FEX submission natsortfiles, which was written to deal with this exact problem: http://www.mathworks.com/matlabcentral/fileexchange/47434-natural-order-filename-sort S = dir('*.txt'); S.name S = natsortfiles(S); % alphanumeric sort by filename S.name