The mannan‐binding lectin (MBL) pathway is part of the innate immune system providing a first line of defence against infections. MBL and ficolins circulate in complexes with MBL‐associated serine proteases (MASP‐1, ‐2 and ‐3). After recognition of a microorganism by MBL, activation of the complement system occurs. MASP‐1 and MASP‐3 share five domains (making up the so‐called A‐chain), whereas they have unique protease domains (B‐chains). Before the identification of MASP‐3, an assay for MASP was presented, based on antibodies against the A‐chain of MASP‐1. With the new knowledge of the three MASPs, and the sharing of domains by MASP‐1 and MASP‐3, assays specific for the protease domains have to be constructed, if one wishes to measure the proteins individually. We present an assay for quantifying total MASP‐3 in plasma and serum samples. The assay is a sandwich‐type assay using as catching antibody a monoclonal antibody against the common A‐chain of MASP‐1/3 and a developing secondary antibody against the C‐terminal part of the protease domain of MASP‐3. We have used this assay for estimating the normal concentration of the protein as well as the concentration in patients and also for characterizing by gel permeation chromatography the MASP‐3 protein in serum.