We studied the performance of three-dimensional fluorescence tomography of diffuse media in the presence of heterogeneities. Experimental measurements were acquired using an imaging system consisting of a parallel plate-imaging chamber and a lens coupled charge coupled device camera, which enables conventional planar imaging as well as fluorescence tomography. To simulate increasing levels of background heterogeneity, we employed phantoms made of a fluorescent tube surrounded by several absorbers in different combinations of absorption distribution. We also investigated the effect of low absorbing thin layers (such as membranes). We show that the normalized Born approach accurately retrieves the position and shape of the fluorochrome even at high background heterogeneity. We also demonstrate that the quantification is relatively insensitive to a varying degree of heterogeneity and background optical properties. Findings are further contrasted to images obtained with the standard Born expansion and with a normalized approach that divides the fluorescent field with excitation measurements through a homogeneous medium.