A derivatization-free hydrophilic-interactive chromatography-mass spectrometry (HILIC-MS/MS) method was developed for quantifying low levels of alendronate in human plasma. Alendronate was separated and concentrated using calcium co-precipitation and analyzed by HILIC-MS/MS, requiring only a 300 μL plasma sample for each analysis. The method is simpler, safer, and more environmentally friendly than the conventional LC-MS/MS method that requires solid-phase extraction and derivatization steps during sample pretreatment. The method was validated for selectivity, linearity, precision, accuracy, extraction recovery, matrix effect and limit of quantification. The between-run precisions were no more than 7.1 % with accuracy ranging from − 1.7–6.3 %; extraction recovery was determined to be 85.3 %; while validation results indicated that the method was suitable for accurately quantifying alendronate concentrations in the range from 0.2 to 50 ng/mL. The approach was used successfully for high throughput analysis of alendronate in more than 3700 plasma samples from 120 subjects in a bioequivalence study.