The models parallel factor analysis (PARAFAC) and the recently introduced bilinear least squares (BLLS) were applied to develop second-order calibration methods to high performance liquid chromatography with diode array detection (HPLC-DAD) data, where overlap of interferences with the compounds of interest was observed, making the determination and resolution of the analytes possible. In this work, the simultaneous determination of five pesticides and two metabolites in wine samples by HPLC-DAD was performed, using the second-order advantage. The results of two chromatographic methods were compared, involving either isocratic or gradient elution. An appropriate preprocessing method was necessary to correct the effects of time shifts, baseline variations and background. BLLS presented results that were of the same quality as PARAFAC in five cases, but in two other situations only PARAFAC enabled analyte quantitation. Relative errors of prediction lower than 10% for all compounds were obtained, indicating that the methodology employing HLPC-DAD and second-order calibration can handle complex analytical systems.