We compared neighbouring regions of the Czech Republic (CZ) and Poland (PL) situated within 100 km of the country border, in order to compare surveillance systems performance in measuring the burden of tick-borne diseases in both countries. We used routine surveillance notifications from 1999-2008 on tick-borne encephalitis (TBE) and Lyme borreliosis (LB). We assessed the crude risk ratio (RR) across the country border, and its estimates adjusted for both population density and the expected epidemiological gradient across the region, using negative binomial regression. The crude RR between CZ and PL was 7.43 (95% Cl 6.20-8.90) for TBE, and 1.80 (1.76-1.83) for LB. The adjusted RR for TBE increased from 4.47 in 1999-2001 to 10.01 in 2005-2008, but for LB decreased from 9.30 to 2.51 during the respective periods. Those results reflect possible differences in surveillance systems performance between the two countries, as the administrative boundaries cannot constitute a barrier for zoonotic diseases and no biological processes alone can explain such large differences in disease occurrence.