Forty-one defendants in total face charges over the collapse of the complex, which housed five garment factories supplying global brands.
Plaza owner Sohel Rana is the principal accused. Public Prosecutor Abdul Mannan said 38 had been charged with murder while three had been charged with helping Rana to flee.
'Rana Plazas everywhere': Danger still haunts Bangladesh
Of the 41 charged, 35, including Rana, who is being held on remand, appeared before the court and pleaded not guilty, Mannan told reporters. The other six will be tried as fugitives from justice.
The collapse of the complex, built on swampy ground outside the capital Dhaka, sparked demands for greater safety in the world's second-largest exporter of readymade garments and put pressure on companies buying clothing from Bangladesh to act.
The duty-free access offered by Western nations and low wages for its workers helped turn Bangladesh's garment exports into an industry with $28 billion in annual revenue.
The minimum monthly wage for garment workers in Bangladesh is $68, compared with about $280 in mainland China, which remains the world's biggest clothes exporter.
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