Thanks for the response folks! I need to determine the EXACT frequency difference between the 2 channels, with frequencies in the 2MHz range. Both frequencies are changing continuously and are close (or equal) all the time. The PIC clock is 20MHz. In my application a single count difference between channels is significant, so the lag caused by coding the Start/Stop on successive program lines will give rise to an error.

From reviewing your replies, it seems to me that the only totally satisfactory solution is to:

1 Gate both channels externally using a pair of AND or NAND gates, enabling these via a spare PIC pin
2 Start both timers in the program
3 Then feed both timers by enabling the gates
4 Disable the gates to stop the feed
5 Then read Timer0 and Timer1.

It's just a shame that we need to add a clunky 14 pin IC to do this trivial job!