In this work, we have compared the selectivity of two commercial molecularly imprinted polymers (AFFINIMIP®SPE Estrogens and AFFINIMIP®SPE Zearalenone) for the extraction of 12 estrogenic compounds of interest (i.e. 17α-estradiol, 17β-estradiol, estrone, hexestrol, 17α-ethynylestradiol, diethylstibestrol, dienestrol, zearalenone, α-zearalanol, β-zearalanol, α-zearalenol and β-zearalenol) from different water samples. High-performance liquid chromatography coupled with ion trap mass spectrometry with electrospray ionization was used for their determination. Results showed that although both molecularly imprinted polymeric cartridges were specifically designed for different groups of analytes (natural estrogens like estradiol in the first case and zearalenone derivatives in the second) they nearly have the same extraction performance (with recovery values in the range 65-101%) for the same analytes in Milli-Q water because of the cross-reactivity of the polymer. However, when more complex water samples were analyzed, it was clear that the behavior was different and that the AFFINIMIP®SPE Estrogens showed less cross-reactivity than the other cartridge. Validation of the proposed methodology with both cartridges revealed that the extraction was reproducible and that the final limits of detection of the proposed method were in the low ng/L range.