Intravesical hyaluronic acid (HA) and chondroitin sulphate (CS) instillation are effective for urinary tract infections (UTIs) and bladder pain syndrome. This study aimed to evaluate the tolerability, safety and efficacy of intravesical HA and CS instillation in patients with late radiation tissue cystitis (LRTC). In this pilot study, tolerability was reported as discontinuation or deviation of the protocol, safety as general or local side effects, efficacy as improvement of bladder capacity and frequency, quality of life (QoL) through the European Quality of Life 5-Dimensions (EQ-5D) (details at http://www.controlled-trials.com/ISRCTN37534393 ). Thirty-two patients with LRTC were enrolled. Twenty-seven patients (84.8%) received a mean of 12.2±0.3 months of instillation therapy. Only two patients (6.2%) developed a urinary tract infection from instillation, which required antibiotic treatment, nevertheless not compromising the therapy schedule. No male patient developed a urethral stricture. Intravesical instillation was associated with a significant increase (>50%) of bladder capacity from baseline (66.9ml) both at 3 months (101.9ml; p<0.001) and 12 months (174.4 ml; p<0.001). EQ-5D index significantly increased from baseline to both 3 and 12 months (0.26, 0.69 and 0.96, respectively; p<0.001). Intravesical co-administration of HA and CS improved bladder function, symptoms and QoL in patients with LRTC.