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Saudi clerics, including those holding official positions, have "vigorously employed" 21st-century tools, like Twitter, to stoke intolerance among millions of followers, the New-York based watchdog said.
Often their words rise to the level of "incitement to hatred or discrimination", it said.
Derogatory statements against Shiites made by influential clerics mirror language found in state-sanctioned religious edicts and even children's schoolbooks, which use widely understood terms to castigate Shiite religious beliefs, HRW said.
The watchdog cited numerous examples, including a Facebook post in which Al-Sharif Hatem bin Aref al-Awni -- a former member of the government's Shura council -- hailed the bombing of a Shiite mosque in Qatif in 2015.
He later removed the post, without explanation.
Anti-Shiite attitudes come from the top.
They point out that such designations are dangerous in a country where apostasy can be punishable by death.
HRW said hate speech against Shiites has had "fatal consequences" across the region, employed by groups including the Islamic State and Al-Qaeda as justification for targeting Shiite civilians and religious sites in Syria, Iraq and elsewhere.
On the contrary, Riyadh had on occasions punished those who attempted to unite Sunnis and Shiites, besides shutting down a committee which was working to unify the Sunni and Shiite lunar calendars.
The US considers Saudi Arabia a country of "particular concern" when it comes to religious persecution, but successive administrations have waived the potential sanctions that come with such a designation.
HRW urged the US, a key Saudi ally, to end the waiver.