Be sure to remember to configure the native VLAN on both sides of the trunk link or you will get this error until you do so (or disable CDP):

*Mar  1 01:35:01: %CDP-4-NATIVE_VLAN_MISMATCH: Native VLAN mismatch discovered on FastEthernet0/13 (1), with sw1 FastEthernet0/13 (10).

They come in once every minute (CDP updates go every 60 seconds by default):

*Mar  1 01:38:01: %CDP-4-NATIVE_VLAN_MISMATCH: Native VLAN mismatch discovered on FastEthernet0/13 (1), with sw1 FastEthernet0/13 (10).
*Mar  1 01:39:01: %CDP-4-NATIVE_VLAN_MISMATCH: Native VLAN mismatch discovered on FastEthernet0/13 (1), with sw1 FastEthernet0/13 (10).
*Mar  1 01:40:01: %CDP-4-NATIVE_VLAN_MISMATCH: Native VLAN mismatch discovered on FastEthernet0/13 (1), with sw1 FastEthernet0/13 (10).

sw2(config-if)#do sh cdp
Global CDP information:
        Sending CDP packets every 60 seconds
        Sending a holdtime value of 180 seconds
        Sending CDPv2 advertisements is  enabled

What happens if you disable CDP?  Will you still get the error?

sw1:
sw1(config)#do sh run int fa0/13
Building configuration…
Current configuration : 128 bytes
!
interface FastEthernet0/13
 switchport trunk encapsulation dot1q
 switchport trunk native vlan 10
 switchport mode trunk
end
sw2:
sw2(config-if)#do sh run int fa0/13
Building configuration…
Current configuration : 110 bytes
!
interface FastEthernet0/13
 switchport trunk encapsulation dot1q
 switchport mode trunk
 no cdp enable
end
***
sw1#sh int fa0/13 trunk
Port        Mode         Encapsulation  Status        Native vlan
Fa0/13      on           802.1q         trunking      10
sw1#sh int fa0/13 switch | i Native VLAN
Administrative Native VLAN tagging: enabled
sw1#sh cdp int fa0/13
FastEthernet0/13 is up, line protocol is up
  Encapsulation ARPA
  Sending CDP packets every 60 seconds
  Holdtime is 180 seconds
sw2#sh int fa0/13 trunk
Port        Mode         Encapsulation  Status        Native vlan
Fa0/13      on           802.1q         trunking      1
sw2#sh int fa0/13 switch | i Native VLAN
Administrative Native VLAN tagging: enabled
sw2#sh cdp int fa0/13
[Note: No output because we've disabled CDP]
sw2#

It’s been a few minutes and no alarms(on either switch):

*Mar  1 01:42:14: %SYS-5-CONFIG_I: Configured from console by console
sw1#sh clo
*01:48:09.468 UTC Mon Mar 1 1993
*Mar  1 01:41:51: %SYS-5-CONFIG_I: Configured from console by console
sw2#sh clo
*01:45:09.826 UTC Mon Mar 1 1993

Another good reason to run CDP. 

Network Bulls
Best Institute for CCNA CCNP CCSP CCIP CCIE R&S, CCIE Security Training in India
www.networkbulls.com
M-44, Old Dlf, Sector-14
Gurgaon, Haryana, india