Two identical triple quadrupole mass spectrometers, operated in the Selected Reaction Monitoring mode, under exactly the same parameters' settings, were employed for the comparison of GC-MS/MS and LC-MS/MS techniques in the analysis of 221 pesticides at low-concentration levels. The comparison was performed with the use of analytical standards' solutions that contained no matrix. The evaluated parameters for the comparison were the applicability, that is, the number of analytes determined by each technique: linearity, sensitivity, repeatability, and confirmation capability. The results of the study indicate that both techniques are equally applicable, as each is capable of determining 167 of the 221 compounds, while 113 of the compounds can be determined by both techniques. The results also show that, although both techniques are very sensitive and selective, GC-MS/MS presents better sensitivity, selectivity, and repeatability at low-concentration levels. But, LC-MS/MS has better linearity characteristics. However, the behavior of certain pesticide classes seems to deviate from these general findings. These results indicate the potential for a wider use of GC-MS/MS in the near future and possibly a simultaneous decline in the use of single quadrupole techniques for the analysis of pesticides at low concentrations.