An ultrasensitive stable isotope dilution liquid chromatography–tandem mass spectrometry method (LC–MS/MS) was developed and validated for multiplexed quantitative analysis of six unconjugated and conjugated estrogens in human serum. The quantification utilized a new derivatization procedure, which formed analytes as pre-ionized N-methyl pyridinium-3-sulfonyl (NMPS) derivatives. This method required only 0.1 mL of human serum, yet was capable of simultaneously quantifying six estrogens within 20 min. The lower limit of quantitation (LLOQ) for estradiol (E2), 16α-hydroxy (OH)-E2, 4-methoxy (MeO)-E2 and 2-MeO-E2 was 1 fg on column, and was 10 fg on column for 4-OH-E2 and 2-OH-E2. All analytes demonstrated a linear response from 0.5 to 200 pg/mL (5–2000 pg/mL for 4-OH-E2 and 2-OH-E2). Using this validated method, the estrogen levels in human serum samples from 20 female patients and 20 male patients were analyzed and compared. The levels found for unconjugated serum E2 from postmenopausal women (mean 2.7 pg/mL) were very similar to those obtained by highly sensitive gas chromatography–mass spectrometry (GC–MS) methodology. However, the level obtained in serum from older men (mean 9.5 pg/mL) was lower than has been reported previously by both GC–MS and LC–MS procedures. The total (unconjugated + conjugated) 4-MeO-E2 levels were significantly higher in female samples compared with males (p < 0.05). The enhanced sensitivity offered by the present method will allow for a more specific analysis of estrogens and their metabolites. Our observations might suggest that the level of total 4-MeO-E2 could be a potential biomarker for breast cancer cases.