In experimental studies on peripheral nerve repair, the possibility to objectively compare original and post-operative innervation is of decisive importance for the selection of the proper nerve-reconstruction strategy. Herewith we report serious drawbacks encountered with the standard method of pre- and post-operative intramuscular injections of widely used retrograde neuronal tracers. Labeling of rat facial motoneurons by injection of Fast-Blue (FB; Group 1), Dil (Group 2), or Fluoro-Gold (FG; Group 3) into the whisker pad muscles was followed by transection and suture of the facial nerve. Two months later, the same rats received Dil (Group 1), FG (Group 2), and FB (Group 3) injections with the same parameters as the pre-operative injections. By quantitative evaluation of single- and double-retrogradely labeled perikarya of facial motoneurons, we tried to estimate the accuracy of re-innervation. Observations through a "UV-filter" (for FB-labeled perikarya) and a "rhodamine-filter" (for Dil-labeled perikarya) in Group 1 revealed an unexpected axotomy-triggered leakage of FB which compromised the counts. After pre-operative Dil labeling, nerve suture, and post-operative FG labeling (Group 2), Dil created an extracellular deposit in the whisker pad. Thus, the uptake of pre-operative tracer by sprouts of re-growing axons compromised counts of retrogradely labeled motoneurons. Employing the "UV-filter" in Group 3 (FG-, FB-, FG+FB-labeled perikarya), the emission of FB obscured that of FG and also compromised cell counts. The use of filter sets constructed ad hoc for detection of FG and FB rendered possible an objective comparison.