Vasco, I am not able to reproduce this on Percona Server 5.5.25a, XtraBackup 2.0.1 - do you can you share your versions, my.cnf and specific procedure - a transcript like mine below can help. [revin@forge msb_5_5_250]$ ./use test Reading table information for completion of table and column names You can turn off this feature to get a quicker startup with -A Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 6 Server version: 5.5.25a-rel27.1 Percona Server with XtraDB (GPL), Release rel27.1, Revision 277 Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql [localhost] {msandbox} (test) > drop table `test-ab`; Query OK, 0 rows affected (0.00 sec) mysql [localhost] {msandbox} (test) > set global innodb_file_per_table=1; Query OK, 0 rows affected (0.00 sec) mysql [localhost] {msandbox} (test) > create table `test-ab` (id int) engine=innodb; Query OK, 0 rows affected (0.01 sec) mysql [localhost] {msandbox} (test) > insert into `test-ab` values(100); Query OK, 1 row affected (0.00 sec) mysql [localhost] {msandbox} (test) > \q Bye [revin@forge msb_5_5_250]$ ls -alh data/test/ total 144K drwx------. 2 revin revin 50 Aug 11 22:34 . drwx------. 5 revin revin 4.0K Aug 11 22:32 .. -rw-rw----. 1 revin revin 8.4K Aug 11 22:34 test@002dab.frm -rw-rw----. 1 revin revin 96K Aug 11 22:35 test@002dab.ibd [revin@forge msb_5_5_250]$ innobackupex --defaults-file=/ssd/msb/msb_5_5_250/my.sandbox.cnf /ssd/msb/msb_5_5_250/bkp/ InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy and Percona Inc 2009-2012. All Rights Reserved. This software is published under the GNU GENERAL PUBLIC LICENSE Version 2, June 1991. 120811 22:35:22 innobackupex: Starting mysql with options: --defaults-file='/ssd/msb/msb_5_5_250/my.sandbox.cnf' --unbuffered -- 120811 22:35:22 innobackupex: Connected to database with mysql child process (pid=14750) 120811 22:35:28 innobackupex: Connection to database server closed IMPORTANT: Please check that the backup run completes successfully. At the end of a successful backup run innobackupex prints "completed OK!". innobackupex: Using mysql Ver 14.14 Distrib 5.5.27, for Linux (x86_64) using readline 5.1 innobackupex: Using mysql server version Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved. innobackupex: Created backup directory /ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28 120811 22:35:28 innobackupex: Starting mysql with options: --defaults-file='/ssd/msb/msb_5_5_250/my.sandbox.cnf' --unbuffered -- 120811 22:35:28 innobackupex: Connected to database with mysql child process (pid=14778) 120811 22:35:30 innobackupex: Connection to database server closed 120811 22:35:30 innobackupex: Starting ibbackup with command: xtrabackup_55 --defaults-file="/ssd/msb/msb_5_5_250/my.sandbox.cnf" --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28 innobackupex: Waiting for ibbackup (pid=14786) to suspend innobackupex: Suspend file '/ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28/xtrabackup_suspended' xtrabackup_55 version 2.0.1 for Percona Server 5.5.16 Linux (x86_64) (revision id: undefined) xtrabackup: uses posix_fadvise(). xtrabackup: cd to /ssd/msb/msb_5_5_250/data xtrabackup: Target instance is assumed as followings. xtrabackup: innodb_data_home_dir = ./ xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend xtrabackup: innodb_log_group_home_dir = ./ xtrabackup: innodb_log_files_in_group = 2 xtrabackup: innodb_log_file_size = 5242880 120811 22:35:30 InnoDB: Using Linux native AIO 120811 22:35:30 InnoDB: Warning: allocated tablespace 10, old maximum was 9 >> log scanned up to (1606945) [01] Copying ./ibdata1 to /ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28/ibdata1 [01] ...done [01] Copying ./test/test@002dab.ibd to /ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28/./test/test@002dab.ibd [01] ...done 120811 22:35:32 innobackupex: Continuing after ibbackup has suspended 120811 22:35:32 innobackupex: Starting mysql with options: --defaults-file='/ssd/msb/msb_5_5_250/my.sandbox.cnf' --unbuffered -- 120811 22:35:32 innobackupex: Connected to database with mysql child process (pid=14800) 120811 22:35:34 innobackupex: Starting to lock all tables... >> log scanned up to (1606945) >> log scanned up to (1606945) 120811 22:35:44 innobackupex: All tables locked and flushed to disk 120811 22:35:44 innobackupex: Starting to backup .frm, .MRG, .MYD, .MYI, innobackupex: .TRG, .TRN, .ARM, .ARZ, .CSM, .CSV and .opt files in innobackupex: subdirectories of '/ssd/msb/msb_5_5_250/data' innobackupex: Backing up files '/ssd/msb/msb_5_5_250/data/mysql/*.{frm,MYD,MYI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (72 files) innobackupex: Backing up file '/ssd/msb/msb_5_5_250/data/test/test@002dab.frm' innobackupex: Backing up files '/ssd/msb/msb_5_5_250/data/performance_schema/*.{frm,MYD,MYI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (18 files) 120811 22:35:44 innobackupex: Finished backing up .frm, .MRG, .MYD, .MYI, .TRG, .TRN, .ARM, .ARZ, .CSV, .CSM and .opt files innobackupex: Resuming ibbackup xtrabackup: The latest check point (for incremental): '1606945' xtrabackup: Stopping log copying thread. .>> log scanned up to (1606945) . xtrabackup: Transaction log of lsn (1606945) to (1606945) was copied. 120811 22:35:47 innobackupex: All tables unlocked 120811 22:35:47 innobackupex: Connection to database server closed innobackupex: Backup created in directory '/ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28' innobackupex: MySQL binlog position: filename '', position 120811 22:35:47 innobackupex: completed OK! [revin@forge msb_5_5_250]$ ls -alh /ssd/msb/msb_5_5_250/bkp/2012-08-11_22-35-28/test/ total 112K drwx------. 2 revin revin 50 Aug 11 22:35 . drwxrwxr-x. 5 revin revin 4.0K Aug 11 22:35 .. -rw-rw----. 1 revin revin 8.4K Aug 11 22:34 test@002dab.frm -rw-rw----. 1 revin revin 96K Aug 11 22:35 test@002dab.ibd