This research investigated the effect of biochemical polymorphisms on performance traits in Nigerian indigenous chicken genotypes. The chickens were obtained from pedigree mating of Normal feathered, Frizzle feathered and Naked Neck cocks to Normal feathered, Frizzle feathered and Naked Neck hens respectively to produce F1 offspring. One hundred and fifty five chicks (37 Frizzle, 79 Normal and 39 Naked Neck) were measured for body weight (g), breast girth (cm) and tibia length (cm). At 20weeks, 5ml of blood was collected from wing vein of each chicken into heparinized tubes labeled according to its tag number for electrophoresis. Each bird was scored as either fast (AA), midway (AB) or slow (BB) according to the mobility on the cellulose-acetate paper for each of transferrin, haemoglobin and carbonic anhydrase. Data obtained were subjected to general linear model procedure of statistical analysis system (SAS, 2002)and significant means were separated using tukey honestly significant difference. Hardy Weinberg‟s equation was used to calculate genotypic and allelic frequencies and tested using chi-square (χ2). Each of the three biochemical markers distinguished into three polymorphic forms viz; AA, AB and BB. The Frizzle feathered had significant higher (P<0.05) weight (338.54g) than both the Normal feathered (319.59g) and Naked Neck (295.51g) from day old to 8weeks, with no significant differences (P>0.05) from 12 to 20 weeks with no consistent trend for tibia length and breast girth. The effect of sexual dimorphism was significant (P<0.05) with males having significantly higher body weight (1168.79g) than females (937.06g), breast girth, males (25.74cm) and females (24.24cm) and tibia length, males (9.59cm) and females (8.96cm). The genotypic frequencies of Transferrin (TfAA, TfAB and TfBB) had 8, 140 and 7 respectively, haemgolobin (HbAA, HbAB and HbBB), had 49, 56 and 50 respectively and carbonic anhydrase (CaAA, CaAB and CaBB) had 63, 79 and 13 respectively. The effect of the polymorphic forms on body weight (g), breast girth (cm), tibia length (cm) showed that the AA had significant higher (P<0.05) body weight (g) than AB and BB for; transferrin (1434.75g, 1047.11g, 1047.43g respectively) and haemoglobin (1296.43g, 1029.59g, and 884.46g respectively). The AA was also higher (P<0.05) than the AB and BB for breast girth (cm) and tibia length (cm) in the case of transferrin and haemoglobin. The carbonic anhydrase showed no consistent significant differences (P>0.05) between the different genotypes for body weight (g), breast girth (cm) and tibia length (cm). It could be concluded that body weight of the genotypes indicated Frizzle feather may be suitable for meat production. The effect of sexual dimorphism showed that the parameters were sex influenced. The high level of heterozygosity indicates that more of the heterozygotes adapted and survived better than the homozygotes. The effect of the polymorphic forms of the biochemical markers on body weight (g), breast girth (cm), and tibia length (cm) showed that transferrin and haemoglobin could be used for body weight selection, while carbonic anhydrase may not be used for selection of the measured parameters.