We present a planar chromatographic separation method for the phytoestrogenic active compound equol, separated on RP-18 W (Merck, 1.14296) phase. It could be shown that an ethanolic cattle manure extract contains this phytoestrogenic active compound to a larger amount. As solvents for the mobile phase, hexane, ethyl acetate, and acetone (45:15:10, v/v); acetone and water (15:10, v/v); and n-hexane, CH2Cl2, ethyl acetate, methanol, and formic acid (40:40:20:5:1, v/v) have been used. After separation, a modified yeast estrogen screen (YES) test was applied, using the yeast strain Saccharomyces cerevisiae BJ3505 containing an estrogen receptor. Its activation by equol induces the reporter gene lacZ which encodes the enzyme β-galactosidase. The enzyme activity is measured directly on the TLC plate by using the substrate MUG (4-methylumbelliferyl-β-d-galactopyranoside) or the substrate X-β-Gal (5-bromo-4-chloro-3-indoxyl-β-d-galactopyranoside). β-Galactosidase cleaves MUG into a fluorescing compound. X-β- Gal is also hydrolyzed and then oxidized by oxygen forming the deep-blue dye 5,5′-dibromo-4,4′-dichloro-indigo. Both reactions in combination with a thin-layer chromatography (TLC) separation allow very specific detecting of equol in cattle manure, although that is a very challenging matrix. Preliminary results show that the average content of equol in liquid manure is roughly 60 μg g−1. The value for urine is 50 μg mL−1.