Sahel sheep and goats, under extensive or semi-intensive management in smallholder farms in semi-arid northeastern Nigeria (Maiduguri), were evaluated to determine the relationship between faecal egg count (FEC) and packed cell volume (PCV) with associated anaemia and whether concurrent haemoparasitic infections would confound the variables. Faecal and anticoagulated blood samples from Sahel sheep (n = 227) and goats (n = 415) were collected January–December 2006, after conjunctival colour was estimated as FAMACHA score (FS) as follows: red (1), red–pink (2), pink (3), pink–white (4) or white (5). Presumed level of helminth infection, based on FEC with modified McMaster technique, was graded as mild (<600/g), moderate (600–1,500/g) or severe (>1,500/g). Out of 642 animals, 276 (43.0 %) had helminth infection based on FEC. More goats (11.5 %) were severely infected than sheep (1.3 %). PCV was decreased by only severe helminth burden. FS correlated with PCV (r = −0.69, −0.86; p < 0.05), but neither FS nor PCV correlated with FEC. Mean FEC was higher at FS = 5 than at FS ≤ 4. More goats (19.3 %) than sheep (9.7 %) were anaemic (normocytic and normochromic) at PCV ≤ 19 %, but percentage decrease of PCV from the control mean was less in goats (22.2 %) than in sheep (36.6 %). PCV was lower in the dry season than the rainy season, but FEC was not significantly affected by season from pooled data. Concurrence of low FEC (<1,000/g) with haemoparasitism (Babesia, 0.8 %; Anaplasma, 5.6 %) was observed in 16 (2.5 %) animals and did not have confounding effects on FEC and PCV. This report has provided preliminary information needed for further evaluation of the diagnostic criteria for helminthiasis and the associated anaemia in a semi-arid environment. © 2013, Springer-Verlag London.