The district court in the western city of Duesseldorf ruled in favour of a man suing the owner of his flat for the full refund of his USD 3,490 deposit, the court said in a ruling obtained by national news agency DPA.
The proprietor had told the tenant he would withhold 1,900 euros because the marble floor of the washroom was permanently stained by splashed urine.
Judge Stefan Hank agreed with an expert's report that it was in fact uric acid that had eaten through the floor but said that standing to urinate was widespread.
"Despite the increasing domestication of men in this area, urinating while standing up is indeed still common practice," Hank said in the ruling.
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"Someone who still practises this previously dominant custom is regularly confronted with significant disputes, particularly with female cohabitants. However normally he must not reckon with damage to the marble floor of a bathroom or guest toilet."
Tenants' rights are a frequent subject of litigation in Germany.
Last June, the same Duesseldorf court ruled that an elderly smoker must vacate his home of around 40 years after neighbours complained about his cigarette smoke.