We investigate the structure of the O-type binary system HD 48099 by measuring linear polarization that arises due to light scattering process. High-precision polarimetry provides independent estimates of the orbital parameters and gives important information on the properties of the system. Linear polarization measurements of HD 48099 in the B, V and R passbands with the high-precision Dipol-2 polarimeter have been carried out. The data have been obtained with the 60cm KVA (Observatory Roque de los Muchachos, La Palma, Spain) and T60 (Haleakala, Hawaii, USA) remotely controlled telescopes during 31 observing nights.Polarimetry in the optical wavelengths has been complemented by observations in the X-rays with the SWIFT space observatory. Optical polarimetry revealed small intrinsic polarization in HD 48099 with 0.1% peak to peak variation over the orbital period of 3.08d. The variability pattern is typical for binary systems, showing strong second harmonic of the orbital period. We apply our model code for the electron scattering in the circumstellar matter to put constraints on the system geometry. A good model fit is obtained for scattering of light on a cloud produced by the colliding stellar winds. The geometry of the cloud, with a broad distribution of scattering particles away from the orbital plane, helps in constraining the (low) orbital inclination. We derive from the polarization data the inclination i=17{deg}+/-2{deg} and the longitude of the ascending node Omega=82{deg}+/-1{deg} of the binary orbit. The available X-ray data provide additional evidence for the existence of the colliding stellar winds in the system. Another possible source of the polarized light could be scattering from the stellar photospheres. The models with circumstellar envelopes, or matter confined to the orbital plane, do not provide good constraints on the low inclination, better than i<=27{deg}, as is already suggested by the absence of eclipses.