Thank you very many, almut ;-). Now I have an efficient way to extract sequences from a fasta file (doing bioinformatics stuff). It is more than 10times faster than the awk oneliner from my first post.
Here is almuts code slighly adjusted. It can be used to extract sequences from a multifasta file.

usage extract-seq.pl file1 file2
cat file1
AV12349
J234054
   .
   .
cat file2
>AV12349
AAACCGTACCTAGAACAGTA
ACAGTACA
>J434594
ACCGTTAGTACGATACA
    .
    .
[download]

file1 contains ID to extract, file2 contains sequences in multifasta format. output will be written
to the file extracted.seqs

#!/usr/bin/perl

$output = "extracted.seqs";

open (OUT,">$output") or die;

# create names lookup table from first file
while (<>) {
    chomp;
    $names{$_} = 1;
    last if eof;
}
$/ = "\n>";  # set input record separator

# scan second file
while (<>) {
     s/^>//;  #remove leading ">"
     s/>$//;  #remove trailing ">"

     if (/^([\w\d]+)/ && $names{$1}) { print OUT ">$_";}

}
[download]