The aim of the present study was to evaluate the effect of patellofemoral joint morphology and patellar alignment (lateral patellar tilt and sagittal patellar tilt) on the presence and stage of CP, and identify the differences between sexes. MRI of 243 patients [146 men (60.1%)] were evaluated retrospectively. Patients were grouped as normal group without chondromalacia, group with mild chondromalacia (grades 1-2) and group with severe chondromalacia (grades 3-4). Sagittal patellofemoral alignment was assessed by the angle between the patella and patellar tendon (P-PTA), and the angle between the quadriceps tendon and patella (Q-PA). Patellar tilt was assessed by lateral patellar tilt angle (LPTA). In addition, patellofemoral joint morphology was evaluated by measuring trochlear depth (TD), trochlear sulcus angle (TSA) and patella angle (PA). P-PTA, Q-PA, LPTA and TD values were significantly lower in patients with severe chondromalacia than in patients with both normal and mild chondromalacia (P < 0.001). TSA values were significantly higher in patients with severe chondromalacia than those with both normal and mild chondromalacia (P < 0.001). TSA was higher and TD was lower in women compared to men (P < 0.001). LPTA and P-PTA were lower in women compared to men, and the difference was significant. There was no difference in PA between the two sexes. Patellar cartilage degeneration increases with trochlear dysplasia. There is a strong correlation between patellar malalignment (lateral patellar tilt and sagittal patellar tilt) and chondromalacia patella. Women are more prone to developing CP than men.