Low birthweight is associated with maternal anaemia and, in some circumstances, with low iron and zinc status, but this relationship has not been investigated in the Philippines. In this study, we assessed the prevalence of anaemia and suboptimal iron and zinc status in pregnant women from three geographical regions (mountain, coast, city) of Zamboanga del Sur province at 24 weeks (n = 305), and again at 36 weeks (n = 127), gestation. At 24 weeks, 34% were anaemic (i.e., haemoglobin < 105 g/L) from all causes, of whom only 14% had concomitant low serum ferritin values (i.e., < 12 μg/L). The presence of infection was low, based on both elevated white blood cell count (> 11 × 109/L; 19%) and serum C-reactive protein (> 15 mg/L; 3%). Of the women surveyed, 20% were iron depleted but not anaemic, and 15% were zinc deficient (i.e., serum zinc < 7.1 μmol/L). The mean (± SD) birthweight of the infants (n = 250) was 3074 g ± 408 g, of whom 5% were of low birthweight (< 2500 g). No differences existed for biochemical indices or birthweight among the three regions, or between women consuming maize or rice-based diets. Women with low haemoglobin (P = 0.05) and low serum zinc (P = 0.14) values at 24 weeks gestation had infants with lower birthweights than those with values ≥ 105 g/L and ≥ 7.1 μmol/L, respectively. However, in the multivariate model, the contribution of maternal haemoglobin to the variance in birthweight at 24 weeks gestation was non-significant, although modest for serum zinc. Anaemia and/or suboptimal zinc status during pregnancy may be related to low birthweight in the Philippines, and their aetiology deserves further study.