Unexplained infertility (UI) was thought to have normal ovulation. To investigate if this is true, ovulation status of UI women were monitored by transvaginal ultrasonography (TVU) during natural cycle. Prospective study. 567 UI women diagnosed with basic infertility evaluation were enrolled to have TVU follicle tracking at an academic fertility center. Their menstrual cycle lengths were 26 to 30 days. The entire follicle development was monitored from day 10 of the cycle to the time of follicle rupture or to day 20 of the cycle. Follicle size was measured and recorded. 421 out of 567 UI women finished 629 natural cycles follicle tracking. In addition to normal follicle size ovulation, three types of abnormal follicular development were observed: 1) no follicular growth in 28 cycles (4.5%); 2) ovulation with small follicles (OSF, follicle ovulate at the size ≤16 mm) in 65 cycles (10.3%); and 3) luteinized unruptured follicles (LUF) in 34 cycles (5.4%). A total of 127 abnormal ovulation cycles were observed in this study, accounting for 20.2% of 629 UI cycles. Based on follicle tracking and timed intercourse, in 502 normal follicle size ovulation cycles 74 women became pregnant while in 65 OSF cycles only 2 became pregnant. The pregnancy rate was 14.7% vs 3.1% (P < 0.01). There was no pregnancy in the 34 LUF and 28 no follicle growth cycle. This study shows ovulation dysfunction existed in UI patients. TVU Follicle tracking is a reliable way to monitor follicle development and ovulation. One cycle of TVU to evaluate ovulation status will make the UI diagnosis more precise.