Purpose The contribution of DWI and FLAIR to the differential diagnosis of type 1, 2, and 3 hydatid cysts and simple liver cysts was investigated according to the Gharbi classification. This study is the first report using FLAIR sequence for the differential diagnosis of liver hydatid cysts in this regard. Methods A total of 82 hydatid cysts and 40 simple cysts were scanned with DWI (in b600-b1000 values) and FLAIR sequence. In 64 patients included in the study, a total of 122 cystic lesions were diagnosed histopathologically or during follow-up. FLAIR and DWI signal characteristics were evaluated, and ADC values were calculated. Results The mean ADC value of hydatid cysts on DWI (b600) was 3.07 ± 0.41 × 10−3 s/mm2, while it was 3.91 ± 0.51 × 10−3 s/mm2 for simple cysts and the difference was statistically significant (p < 0.05). On b1000 DWI, the mean ADC values of hydatid and simple cysts were 2.99 ± 0.38 × 10−3 s/mm2 and 3.43 ± 0:29 × 10−3 s/mm2, respectively (p < 0.05). The qualitative evaluation of the signal intensity on b600−1000 DWI demonstrated the difference between the simple and hydatid cyst groups (p < 0.05). Type 2 hydatid cysts alone were distinguished from type 2–3 hydatid and simple cysts by FLAIR (p < 0.05). Conclusions ADC values can distinguish between hydatid cyst and simple cyst. FLAIR contributes to the differentiation of type 2 hydatid and simple cysts.