I'm able to verify this as described. percona1> select * from irfan; +------+ | id | +------+ | 101 | | 102 | | 103 | | 104 | +------+ 4 rows in set (0.00 sec) From other cluster nodes: percona2> select * from test.irfan; +------+ | id | +------+ | 1 | | 2 | | 3 | | 4 | +------+ 4 rows in set (0.00 sec) [root@percona1 ~]# pt-table-checksum --empty-replicate-table --replicate percona.checksums --ignore-databases=mysql h=192.168.70.2,u=checksum_user,p=checksum_password --recursion-method=cluster Not checking replica lag on percona4 because it is a cluster node. Not checking replica lag on percona2 because it is a cluster node. Not checking replica lag on percona3 because it is a cluster node. TS ERRORS DIFFS ROWS CHUNKS SKIPPED TIME TABLE 08-16T14:28:26 0 0 6 1 0 0.753 sys.sys_config 08-16T14:28:26 0 0 2 1 0 0.118 test.consistency 08-16T14:28:26 0 0 4 1 0 0.148 test.irfan 08-16T14:28:27 0 0 1 1 0 0.407 test.m_deliver 08-16T14:28:27 0 0 1 1 0 0.173 test.m_facility 08-16T14:28:27 0 0 1 1 0 0.089 test.m_facility_history_action 08-16T14:28:27 0 0 0 1 0 0.093 test.m_fqdn 08-16T14:28:27 0 0 1 1 0 0.084 test.m_map_class 08-16T14:28:32 0 0 100000 8 0 4.541 test.sbtest1 08-16T14:28:38 0 0 497446 10 0 5.877 test.t1 08-16T14:28:38 0 0 6 1 0 0.184 test.t2 08-16T14:28:38 0 0 1 1 0 0.455 test.t3 08-16T14:28:38 0 1 3 1 0 0.198 test.t4 08-16T14:28:39 0 0 1 1 0 0.097 test.t_facility_history [root@percona1 ~]# pt-table-checksum --replicate percona.checksums --ignore-databases=mysql h=192.168.70.2,u=checksum_user,p=checksum_password --recursion-method=dsn=D=percona,t=dsns Not checking replica lag on percona2 because it is a cluster node. Not checking replica lag on percona3 because it is a cluster node. Not checking replica lag on percona4 because it is a cluster node. TS ERRORS DIFFS ROWS CHUNKS SKIPPED TIME TABLE 08-16T14:39:57 0 0 4 1 0 0.192 percona.dsns 08-16T14:39:57 0 0 6 1 0 0.248 sys.sys_config 08-16T14:39:57 0 0 2 1 0 0.277 test.consistency 08-16T14:39:58 0 0 4 1 0 0.367 test.irfan 08-16T14:39:58 0 0 1 1 0 0.206 test.m_deliver 08-16T14:39:58 0 0 1 1 0 0.211 test.m_facility 08-16T14:39:58 0 0 1 1 0 0.210 test.m_facility_history_action 08-16T14:39:59 0 0 0 1 0 0.152 test.m_fqdn 08-16T14:39:59 0 0 1 1 0 0.185 test.m_map_class 08-16T14:40:01 0 0 100000 9 0 2.276 test.sbtest1 08-16T14:40:07 0 0 497446 11 0 5.487 test.t1 08-16T14:40:07 0 0 6 1 0 0.261 test.t2 08-16T14:40:07 0 0 1 1 0 0.257 test.t3 08-16T14:40:08 0 1 3 1 0 0.627 test.t4 08-16T14:40:08 0 0 1 1 0 0.278 test.t_facility_history Also, as mentioned in bug report with single row update it showing the DIFFs correctly. percona1> select * from test.irfan; +------+ | id | +------+ | 101 | | 2 | | 3 | | 4 | +------+ 4 rows in set (0.00 sec) while other nodes: percona2> select * from test.irfan; +------+ | id | +------+ | 1 | | 2 | | 3 | | 4 | +------+ 4 rows in set (0.00 sec) [root@percona1 ~]# pt-table-checksum --empty-replicate-table --replicate percona.checksums --ignore-databases=mysql h=192.168.70.2,u=checksum_user,p=checksum_password --recursion-method=cluster Not checking replica lag on percona4 because it is a cluster node. Not checking replica lag on percona2 because it is a cluster node. Not checking replica lag on percona3 because it is a cluster node. TS ERRORS DIFFS ROWS CHUNKS SKIPPED TIME TABLE 08-16T14:46:57 0 0 4 1 0 0.108 percona.dsns 08-16T14:46:57 0 0 6 1 0 0.102 sys.sys_config 08-16T14:46:58 0 0 2 1 0 0.102 test.consistency 08-16T14:46:58 0 1 4 1 0 0.097 test.irfan 08-16T14:46:58 0 0 1 1 0 0.140 test.m_deliver 08-16T14:46:58 0 0 1 1 0 0.107 test.m_facility 08-16T14:46:58 0 0 1 1 0 0.246 test.m_facility_history_action 08-16T14:46:59 0 0 0 1 0 0.334 test.m_fqdn 08-16T14:46:59 0 0 1 1 0 0.349 test.m_map_class 08-16T14:47:02 0 0 100000 9 0 2.707 test.sbtest1 08-16T14:47:09 0 0 497446 14 0 6.980 test.t1 08-16T14:47:09 0 0 6 1 0 0.153 test.t2 08-16T14:47:09 0 0 1 1 0 0.176 test.t3 08-16T14:47:09 0 1 3 1 0 0.157 test.t4 08-16T14:47:09 0 0 1 1 0 0.349 test.t_facility_history [root@percona1 ~]# pt-table-checksum --version pt-table-checksum 3.0.4