E1 and E2 are considered as the parent natural estrogens (NEs) in human metabolism pathways of NEs, while the enantiomer of E2, αE2 was not included and ignored. In this study, αE2 along with the other eleven NEs with estrogenic activities were found in six healthy human urines with the total concentration levels of 62.9–99.3 μg/L. The concentration contributed ratios (CCRs) of αE2 to the total twelve NEs ranged from 4.7% to 11.0% with an average CCR of 7.0%. On the basis of the average CCR, αE2 was 1.5 times that of E2, which suggested that αE2 was one important NE in humans. As the main source of NEs in municipal wastewater was derived from human urine, αE2 should also be an important NE in municipal wastewater that can be proven by previous limited studies, in which the municipal effluent concentrations of αE2 ranged from not detection to 144.2 ng/L with an average concentration of 11.9 ng/L, indicating αE2 in municipal effluent was an important source to the natural environment. Although αE2 is a NE with weak estrogenic potency, the estrogenic effect of αE2 via municipal effluent to its receiving water body cannot be ignored because it can be bio-transformed into E2 under aerobic environment. This work is the first to indicate that αE2 is an ignored NE in human and its environmental risk via municipal effluent discharging cannot be ignored, which should be paid with attention.