Morphometric analyses of endobronchial biopsies are commonly performed in asthma research but little is known about the technical and physiological parameters contributing to measurement variability. We investigated factors potentially affecting biopsy size, quality, and airway smooth muscle (ASM) content in heaves, an asthma-like disease of horses. Horses with heaves in clinical exacerbation (n = 6) or remission (n = 6) from the disease and six controls were studied using a crossover design. The effect of disease status, age, bronchodilation, biopsy forceps type, and carina size on total biopsy area (Atot), ASM area (AASM), ASM% (AASM/Atot), and histologic quality were assessed. Concordance among different measuring techniques was also assessed. Compared with other groups, horses with heaves in exacerbation yielded larger biopsies (P < 0.05). Better quality biopsies were obtained from carinae of small size compared with large ones (P = 0.02), and carina size and forceps type significantly affected the ASM content of the biopsy (interaction, P < 0.05). AASM increased with age only in heaves-affected horses (r = 0.9, P < 0.05), and ASM% was negatively correlated with pulmonary resistance at 5 Hz in heaves-affected horses (r = -0.74, P = 0.01), likely because of the increased thickness of the extracellular matrix layer in this group (P = 0.01). In conclusion, disease status, carina thickness, and the forceps used may significantly affect biopsy size, quality, and ASM content. Endobronchial biopsies are not appropriate samples for ASM quantification in heaves, and studies measuring ASM mass should not be compared when measuring techniques differ.