Background This study aimed to evaluate the imaging findings of patients who underwent an abdominal and pelvic magnetic resonance imaging (MRI) due to primary amenorrhea. Methods The pelvic and abdominal images of 34 female patients (mean age 15.61 years, range 14–19 years) were retrospectively analyzed by a single radiologist blinded to the clinical and laboratory data of the patients (other than primary amenorrhea) to evaluate the etiology of primary amenorrhea. The anatomy and anomalies of the internal genital organs and other accompanying abdominopelvic anomalies were investigated. Results Gonadal dysgenesis was present in 14 patients (41.17%) and Müllerian duct anomalies (MDAs) were present in 20 (58.83%) (Mayer-Rokitansky-Kuster-Hauser [MRKH] syndrome in 13 [65%], distal vaginal obstruction [DVO] findings in five [25%], and obstructed hemivagina and ipsilateral renal anomaly [OHVIRA] syndrome in two [10%]). Seven patients with MRKH (53.84%) were of type 1 and six (46.15%) were of type 2. A total of eight additional anomalies (vertebral and renal) were detected, six in MRKH and two in OHVIRA syndrome cases. Endometrioma and hematosalpinx were observed in one of the five patients with DVO (5%). Conclusions Primary amenorrhea is a common symptom that affects both the physical and psychosocial status of individuals. Determination of the underlying etiology is the first step in planning treatment. The evaluation of internal genital organ anomalies involved in the etiology is important for sexual function and fertility. MRI is a non-invasive imaging modality that should be preferred in these cases as it provides detailed data about the anatomy and anomalies of internal genital organs due to its high soft tissue contrast resolution.