Abstract. Some BL Lacertae objects show a periodic behaviour in their light curves that is often attributed to the orbital motion of a central binary black hole system. On this basis, and assuming a circular orbit, Rieger & Mannheim (2000) have recently proposed a method to determine the orbital parameters of the binary system from the observed quantities, i.e. the signal periodicity, the flux ratio between maximum and minimum signal and the power law spectral index of the photon flux. However, since these binary black holes are expected to originate from galactic mergers, they could well be on eccentric orbits, which might not circularize for a substantial time. We therefore generalize the treatment proposed by Rieger & Mannheim (2000) by taking into account the effect of the orbital eccentricity of the binary system. We apply the model to three well-observed Markarian objects: MKN 501, MKN 421 and MKN 766 that most likely host a binary system in their centers. Some astrophysical implications of this model are also investigated with particular emphasis to the gravitational radiation emission from the binary black holes. Under particular conditions (e.g. for some values of the orbital separation, eccentricity and Lorentz factor) one can obtain signals above the sensitivity threshold of the LISA detector.