Hydrophilic interaction chromatography (HILIC) has, in recent years, been shown to be an important supplement to reversed-phase liquid chromatography for polar analytes. HILIC, in conjunction with tandem mass spectrometry (MS/MS), has been steadily gaining acceptance in the analysis of polar compounds from complex biological matrices. This hyphenated technique offers the advantages of improved sensitivity by employing high organic content in the mobile phase, shortened sample preparation time with direct injection of the organic-solvent extracts of biological samples and the potential for ultra-fast analysis because of low-column backpressure. This article reviews recent challenges presented by HILIC, advancements in the better understanding of retention characteristics of analytes with different mobile- and stationary-phase compositions and solutions to ion suppression and interference problems encountered in HILIC-MS/MS assays. Applications of HILIC-MS/MS are summarized, including those for pharmacokinetic studies, metabolic studies, therapeutic drug monitoring and clinical diagnostics.