Circadian expression rhythms of clock gene products in the bladder are reportedly hindered by clock gene abnormalities. However, the role of clock gene products in various pathological lower urinary tract conditions is unknown. The present study examined the relationship between clock genes and voiding dysfunction in spontaneous hypertensive rats (SHR). The voluntary voiding behavior study using metabolic cages was performed in 18-weeks old male Wistar rats (control group, n = 36) and SHR (SHR group, n = 36) under 12-h light/12-h dark conditions. Bladders were harvested every 4 h at six time points (n = 6 for each time point for each group), and we analyzed the messenger RNA (mRNA) expression of several clock genes: period 2 (
Per2
), cryptochrome 2 (
Cry2
), brain and muscle aryl hydrocarbon receptor nuclear translocator-like protein 1 (
Bmal1
), circadian locomotor output cycles kaput (
Clock
), nuclear receptor subfamily 1, group D, member 1 (
Rev-erbα
), mechanosensors: transient receptor potential vanilloid channel 1 (
TRPV1
),
TRPV4
,
Piezo1
, and vesicular nucleotide transporter (
VNUT
) using real-time polymerase chain reaction. Though 24-h urination frequency for both light and dark periods was significantly higher in the SHR group, urine volume per voiding was significantly lower versus control. In controls, urine volume per voiding was significantly lower during the dark period (active phase) than the light period (rest phase); this parameter did not significantly differ between active and rest phases for SHR. SHR bladders showed significantly higher expression of
Cry2
and
Clock
during the active phase compared to controls. In the SHR group,
TRPV1
,
TRPV4
,
Piezo1
, and
VNUT
mRNA levels were significantly higher during the active phase compared to the control group. We speculate that Cry2 and Clock may be contributing factors in the decrease of bladder capacity during the active phase in SHR through increase of
TRPV1
,
TRPV4
,
Piezo1
, and
VNUT
expression, but further research will be necessary to elucidate the precise mechanisms.