The aim of this study was to evaluate whether salivary contamination during placement of implants with different surface characteristics affects osseointegration in native and in augmented bone areas. Forty eight implants with machined surface (MS) and 48 implants with moderately rough surface (RS) were tested in the calvaria of 12 sheep. At the first surgery, 64 bony critical defects were randomly created and were subsequently augmented with two materials (autogenous or bovine bone). After 5 weeks of graft healing, 8 implants were placed per sheep, in native bone and in the centre of the augmented defects. Forty eight implants were soaked with saliva before placement (contaminated group [CG]), while 48 implants were not (non-contaminated group [NCG]). Five weeks after implant placement, bone-to-implant contact (BIC) and bone material area fraction occupancy (BMAFO) were calculated histomorphometrically. Saliva contamination showed a significant negative effect (p=.000) on BIC, especially in augmented areas. RS showed significant positive effect on BIC, compared to MS (p=.000), while there were no significant differences for different bone conditions (p=.103). For BMAFO, the contamination showed a significantly negative affect (p=.000), while there were no significant differences for surface characteristics (p=.322) and for bone condition (p=.538). Saliva contamination during dental implant placement has a negative effect on osseointegration in augmented areas. Moderately rough surface has a possible advantage in the aspect of initial bone to implant contact. However, it seems to be advisable to avoid saliva contamination especially for implants placed in augmented bone areas.