Quantitative information about the innervation is essential to analyze the structure-function relationships of organs. So far, there has been no unbiased stereological tool for this purpose. This study presents a new unbiased and efficient method to quantify the total length of axons in a given reference volume, illustrated on the left ventricle of the mouse heart. The method is based on the following steps: 1) estimation of the reference volume; 2) randomization of location and orientation using appropriate sampling techniques; 3) counting of nerve fiber profiles hit by a defined test area within an unbiased counting frame on paraffin sections stained immunohistochemically for protein gene product 9.5; 4) electron microscopic estimation of the mean number of axon profiles contained in one nerve fiber profile; 5) estimation of the degree of tissue shrinkage of specimens in paraffin; and 6) calculation of the total axon length within the reference volume, taking tissue shrinkage into account. In a set of five mouse hearts, the total length of axons ramifying between cardiomyocytes ranged between approximately 50 and 100 m, with a mean of 75.98 m (SD 23.73). The time required for the microscopical analysis was approximately 8 h/animal for an experienced observer. Using antibodies specific for different neuron subtypes and immunoelectron microscopy, this method is also suited to estimate the total axon length of neurons expressing different transmitters. This new and efficient method is particularly useful when structural remodeling takes place and is suspected to involve gain or loss of axons.