This study compared the osseointegration of acid-etched, ultrahydrophilic, micro- and nanostructured implant surfaces (ANU) with non-ultra-hydrophilic, microstructured (SA) and non-ultrahydrophilic, micro- and nanostructured implant surfaces (AN) in vivo. Fifty-four implants (n = 18 per group) were bilaterally inserted into the proximal tibia of New Zealand rabbits (n = 27). After 1, 2, and 4 weeks, bone-implant contact (BIC, %) in the cortical (cBIC) and spongious bone (sBIC), bone chamber ingrowth (BChI, %), and the supra-crestal, subperiosteal amount of newly formed bone, called percentage of linear bone fill (PLF, %), were analyzed. After one week, cBIC was significantly higher for AN and ANU when compared to SA (p = 0.01 and p = 0.005). PLF was significantly increased for ANU when compared to AN and SA (p = 0.022 and p = 0.025). After 2 weeks, cBIC was significantly higher in SA when compared to AN (p = 0.039) and after 4 weeks, no significant differences in any of the measured parameters were found anymore. Ultrahydrophilic implants initially improved osseointegration when compared to their non-ultrahydrophilic counterparts. In accordance, ultrahydrophilic implants might be appropriate in cases with a necessity for an accelerated and improved osseointegration, such as in critical size alveolar defects or an affected bone turnover.