An investigation into capillary-scale ion chromatography with suppressed conductivity detection is presented for the identification of low molecular weight anions in samples of limited size. Both particle-packed and polymer monolith capillary ion exchange resins were compared with respect to their chromatographic efficiencies, operating back-pressures and thermal selectivities. Using a multistep hydroxide gradient, it was possible to separate a large selection of inorganic and organic anions in <23 mins using both phases with an injection volume of only 0.4 μL. Method performance was tested with respect to linearity, range, reproducibility and sensitivity and compared to a micro-bore (2 mm) IC method. Limits of mass sensitivity improved by factors up to 1,800-fold using the capillary IC system and lay in the range 0.3–26.2 pg. The finalised analytical method was applied to the determination of both endogenous and exogenous species in sweat and fingermark deposits. It was possible to determine presence of elevated levels of thiocyanate and benzoate in the sweat of three moderate smokers (5–10 cigarettes/day) in comparison to non-smokers. A controlled firing experiment was also conducted to assess the transfer of gunshot residue into fingerprints of a firer. Similarly, identification of direct contact with a black powder substitute is presented via analysis of latent fingermarks. To the best of our knowledge, this represents the first study of sweat and fingerprints using capillary-scale suppressed ion chromatography.