Cellulitis: This is a common cause of penile shaft swelling in children, often resulting from a bacterial infection. The absence of injury makes a traumatic cause less likely, pointing towards an infectious etiology.

Contact Dermatitis: Allergic reactions or irritant dermatitis from soaps, lotions, or other substances can cause swelling and inflammation of the penile shaft.
Balanitis: Inflammation of the glans penis, which can extend to the shaft, often due to poor hygiene, infection, or an allergic reaction.
Urethritis: Inflammation of the urethra, which can cause swelling and discomfort in the penile area, though it's less common in prepubertal boys without a history of sexual activity.

Testicular Torsion: Although it primarily affects the testicles, severe cases can lead to swelling that might be perceived as involving the penile shaft. It's a surgical emergency.
Epispadias or Hypospadias Complications: Though these are congenital conditions, complications or undiagnosed cases could present with swelling, especially if there's an associated urinary tract infection or obstruction.
Malignancy: Rare in children, but penile cancer or other malignancies affecting the genital area could present with swelling and must be considered to ensure prompt treatment.

Henoch-Schönlein Purpura (HSP): A systemic vasculitis that can cause skin lesions, joint pain, and abdominal pain, and rarely, genital swelling.
Behçet's Disease: A rare condition characterized by recurrent oral ulcers, genital ulcers, and uveitis, which could potentially cause penile swelling.
Sarcoidosis: A condition that can affect multiple parts of the body, including the skin, and very rarely might cause genital swelling.