Treatment of B12 deficiency is important to prevent progressive neurological and/or hematologic disease but requires a secure diagnosis. The aim of this study was to evaluate second line tests of B12 status as prognostic indicators of a hematologic response to vitamin B12 therapy. Forty-nine patients referred with low, serum vitamin B12 concentrations were treated with intramuscular B12 and re-assessed after 3 months. Methylmalonic acid, homocysteine, holotranscobalamin and neutrophil hypersegmentation index were measured before and after treatment. Before treatment 27/49 patients were anemic or macrocytic of whom 15 had a clear hematologic response. All the tests had a similar prognostic accuracy. Symptomatic improvement did not correlate with hematologic response. Supplementary tests of vitamin B12 status were not significantly better than total serum B12 concentration as predictors of a hematologic response to vitamin B12 therapy.