In the course of on-farm welfare assessment, behaviour is usually directly observed without extensive habituation periods. It was therefore the aim of this study to investigate the observer effect during direct observations on the behaviour of fattening pigs. In total 546 fatteners (four to six months old) on four organic fattening pig farms with housing systems with straw bedding were observed. Behaviour of pigs was videotaped on two days per farm when direct observations according to the Welfare Quality® protocol were simulated. During two further days video recordings took place without the presence of the observer. All data were collected by indirect observation from the video material. Recording methods were scan sampling and continuous recording. Following the Welfare Quality® protocol, scan sampling (2min intervals) was carried out to assess basic activity (lying, sitting, standing/moving), exploratory behaviour (features of the pen, enrichment material) and social behaviour. Additionally, continuous behaviour sampling was used to record social behaviour and comfort behaviour (stretching, shaking, rubbing and yawning). When the observer was present, sitting and standing/locomotion increased, whilst lying and motionless lying decreased significantly. Exploratory behaviour directed towards straw and eating/drinking increased in the presence of the observer. There was no observer effect on social interactions (negative and positive social interactions). The incidence of stretching was also reduced, while the frequency of rubbing and shaking increased. The observer effect was not significantly reduced by extending the habituation period to 15 minutes, except for drinking behaviour. Exploration of the pen features also tended to return to baseline values with increased habituation period. Welfare Quality® criterion-scores ‘expression of social behaviours and ‘expression of other behaviours derived from data with or without observer presence did not differ. The observer effect should be considered when designing on-farm studies including direct observations and interpreting respective data. It was not minimised by extending the habituation period to 15 min.