Background The objective of this study was to investigate the association between average daily gain and the number of Lawsonia intracellularis bacteria in faeces of growing pigs with different levels of diarrhoea. Methods A longitudinal field study (n?=?150 pigs) was performed in a Danish herd from day 29 to 47 post weaning. Every third day all pigs were weighed, subjected to a clinical examination and faecal samples were obtained. Faecal samples were subjected to dry matter determination and absolute quantification by PCR for L. intracellularis and porcine circovirus type 2 (PCV2). Association between average daily gain, faecal dry matter content, numbers of L. intracellularis bacteria and PCV2 genome copies in faeces was investigated in a multilevel mixed-effects linear model. Results Increasing numbers of L. intracellularis log10 bacteria/g faeces were significantly associated with decreasing average daily gain (P?<?0.001). The association was decreasing with increasing faecal dry matter content (P?<?0.01). The number of PCV2 log10 copies/g faeces was not significantly associated with average daily gain of the pigs (P?>?0.5). Conclusion The results suggest a potential application of a PCR quantifying L. intracellularis in growing pigs. Faecal dry matter content must be taken into consideration in interpretation of such test results.