Antibiotics are frequently administered prophylactically in spinal procedures to reduce the risk of disc space infection. There is still controversy, however, over which antibiotics are able to penetrate the intervertebral disc effectively and whether the charges on the antibiotics are important in determining their ability to diffuse into the negatively charged intervertebral disc. In a prospective randomised double blind clinical study, we examined the penetration of two commonly used antibiotics, cefuroxime (negatively charged) and gentamicin (positively charged), into the intervertebral discs. Twenty patients, randomised into two separate groups, received either 1.5g cefuroxime or 5 mg/kg gentamicin prophylactically two hours before their intervertebral discs removed. A blood specimen, from which serum antibiotic levels were determined, was obtained simultaneously with each discectomy. Clinical therapeutic levels of antibiotic were detectable in the intervertebral discs of all the ten patients who received gentamicin. Only two of the ten patients (20%) who received cefuroxime had quantifiable level of antibiotic in their discs even though serum levels of cefuroxime were at therapeutic levels in all ten patients. Our results showed that cefuroxime does not diffuse into human intervertebral discs as readily as gentamicin and suggest that the charge due to ionisable groups on the antibiotics is important in determining the penetration of antibiotics. We therefore recommend the use of gentamicin in a single prophylactic dose for all spinal procedures to reduce the incidence of post-operative discitis.